I have noticed that after creating a mobile menu based on the Main Menu my Main Menu links no longer contained the "current" and "active" styling. So instead of the menu item reading:

li#current.active.item40

<li id="current" class="active item40"><a href="/index.php/contact"><span>Contact</span></a></li>


It reads only:

li.item40

Mobile Joomla component warns against identical aliases in menu, but how do I duplicate the Main menu without creating identical aliases?

I figured it out. You simply create a new menu and choose Alias in the Menu Item Manager when creating a new menu item.